I'm using the theme-check plugin to check my theme for errors and recommendations, I'm using get_template_part() in theme files like header.php and index.php but in functions.php I'm using include_once() theme-check is not pointing at these, it's pointing at include_once used in a widgets.php file which is included in functions.php

my question is should we use get_template_part() instead of all include_once() and include() or just use it for getting frequently used markup only ? I know it's only recommended to use get_template_part() but I like to follow best practices and recommendations.

Looking at plugin code from some of the core contributors and other WP experts, I've never seen get_template_part() used this way although it doesn't seem wrong. The point of the function, though, is to reuse parts of code which would differentiate it from the need to include a file once. I'm interested in seeing what others have to say about this.
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developdalyApr 7 '12 at 14:23

Those are recommendations, if you're not including template part it's more simple to use include_once().
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MamadukaApr 7 '12 at 14:56